Wow, an old thread revived a bit. I'm properly chastened of course.
Here is where I was coming from. As a beginner it seems strange to practice one fingering pattern on scales, but then notice that in the beginner pieces you are doing, you will never use the same fingering patterns. Of course you aren't doing full scales in most pieces, but certainly shorter segments of scales make up a good bit of music. So what really drives this question is probably the beginner ignorance of the "why" to fingering choices, not the ignorance of scales. Example at the end.
A few people have pointed out the general importance of scales. I agree.
A few have pointed out some specific examples of actual scale fingerings in the music. Okay, good information. Certainly the exception, at my level, but it's good to know they exist.
I understand more today than I did two months ago when I first posted. My confusion will probably continue to decrease as my understanding of fingering choices improves. At this stage I have no set of rules to apply when fingerings aren't written in the music. For example, last night I was looking at the Scarlatti K.32, writing fingerings lightly in pencil (later I'll ask someone how close I came.) It's in D min, I could default to right hand fingerings for F maj. I doubt if there's a single measure where that would make sense though.